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| Cluster | Chromosome | Count | Expected | log2FE | Adjusted.pvalue |
|---|---|---|---|---|---|
| Cluster023 | Chr1 | 9 | 2.25 | 2.00 | 1.161e-02 |
| Cluster004 | Chr4 | 129 | 47.29 | 1.45 | 7.434e-24 |
| Cluster022 | Chr4 | 14 | 5.03 | 1.48 | 1.156e-02 |
| Cluster037 | Chr4 | 23 | 3.35 | 2.78 | 9.033e-14 |
| Cluster084 | Chr4 | 9 | 1.48 | 2.61 | 1.659e-04 |
| Cluster074 | Chr12 | 8 | 0.48 | 4.05 | 6.337e-07 |
Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).
| Cluster | Freq | |
|---|---|---|
| 4 | Cluster004 | 121 |
| 37 | Cluster037 | 18 |
| 22 | Cluster022 | 14 |
| 84 | Cluster084 | 6 |
Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).
The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.
| Cluster | Category | Count | Expected | log2FE | pvalue | adjusted.pvalue |
|---|---|---|---|---|---|---|
| Cluster004 | Chr4ZnF | 121 | 8.34 | 3.86 | 4.243e-100 | 2.546e-99 |
| Cluster022 | Chr4ZnF | 14 | 0.89 | 3.98 | 1.608e-13 | 9.647e-13 |
| Cluster037 | Chr4ZnF | 18 | 0.59 | 4.93 | 3.500e-23 | 2.100e-22 |
| Cluster084 | Chr4ZnF | 6 | 0.26 | 4.53 | 1.201e-07 | 7.206e-07 |
Table showing clusters with significant enrichments (adjusted p-value < 0.05).
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Histogram showing the distribution of genes in clusters 4, 22, 37 and 84.
Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).
Histogram showing the distribution of genes in clusters 4, 22, 37 and 84, split by cluster.
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Histogram of Pearson coefficients between paralogous gene pairs (binwidth = 0.1)
Histogram of Pearson coefficients of a random selection of 3000 genes pairs.
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] rgl_0.96.0 qvalue_2.4.2
## [3] genefilter_1.54.2 DESeq2_1.12.4
## [5] SummarizedExperiment_1.2.3 htmlTable_1.6
## [7] biomaRt_2.28.0 Rgraphviz_2.16.0
## [9] gridExtra_2.2.1 topGO_2.24.0
## [11] SparseM_1.7 GO.db_3.3.0
## [13] graph_1.50.0 cba_0.2-17
## [15] proxy_0.4-16 RColorBrewer_1.1-2
## [17] plyr_1.8.4 GenomicFeatures_1.24.5
## [19] AnnotationDbi_1.34.4 Biobase_2.32.0
## [21] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
## [23] IRanges_2.6.1 S4Vectors_0.10.3
## [25] BiocGenerics_0.18.0 scales_0.4.0
## [27] reshape2_1.4.1 ggplot2_2.1.0
## [29] rprojroot_1.0-2 knitr_1.14
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.0 splines_3.3.1
## [3] Formula_1.2-1 shiny_0.13.2
## [5] highr_0.6 latticeExtra_0.6-28
## [7] Rsamtools_1.24.0 yaml_2.1.13
## [9] RSQLite_1.0.0 lattice_0.20-33
## [11] chron_2.3-47 digest_0.6.10
## [13] XVector_0.12.1 colorspace_1.2-6
## [15] httpuv_1.3.3 htmltools_0.3.5
## [17] Matrix_1.2-6 XML_3.98-1.4
## [19] zlibbioc_1.18.0 xtable_1.8-2
## [21] BiocParallel_1.6.6 annotate_1.50.0
## [23] nnet_7.3-12 mime_0.5
## [25] survival_2.39-5 magrittr_1.5
## [27] evaluate_0.9 foreign_0.8-66
## [29] tools_3.3.1 data.table_1.9.6
## [31] formatR_1.4 matrixStats_0.50.2
## [33] stringr_1.1.0 munsell_0.4.3
## [35] locfit_1.5-9.1 cluster_2.0.4
## [37] Biostrings_2.40.2 RCurl_1.95-4.8
## [39] htmlwidgets_0.7 labeling_0.3
## [41] bitops_1.0-6 rmarkdown_1.0
## [43] gtable_0.2.0 DBI_0.5
## [45] R6_2.1.3 GenomicAlignments_1.8.4
## [47] rtracklayer_1.32.2 Hmisc_3.17-4
## [49] stringi_1.1.1 Rcpp_0.12.6
## [51] geneplotter_1.50.0 rpart_4.1-10
## [53] acepack_1.3-3.3